Spy on a plane
by Ratchet9Cooper
Summary: After a hidden base is attacked by a group of stealthy assassins S.H.I.E.L.D. is contacted by a team of eight mercenaries who say their 9th member has one AWOL, S.H.I.E.L.D ignores this warning, until soon after, Coulson's team is transporting some other agents after a mission, and one by one, they start to disappear. Some minor Fitz/Simmons.
1. The infiltration

A/N: First off, don't own either universe (tf2 or agents of shield)

Just want to clear a few things up before the story. First, this fanfic operates in the TF2 gameplay universe. By that I mean there are multiple Spies, Pyros, Heavies, etc. but there are still a main spy, heavy, etc. Also This takes place before episode 16 in agents of shield. So the major event has happened yet. Also it takes place after episode 14 only because Agent Garrett and Agent Triplett appear. No spoilers after episode 3 or so.

* * *

S.H.I.E.L.D Research and development command post Beta

Location classified, 01:27 A.M.

Lookout duty, a mind dulling boring job to do at a high security base in the middle of the desert, with few people knowing it even exists, let alone where it is. It is terribly boring. Until you hear gunshots in the distance. This is exactly what the guards where thinking, listening to the sounds of guns echoing through the desert. Followed by a slamming noise, as if someone had been slammed into a large truck. Then silence.

The guards waited with uncertainty in the silence, tense with weapons drawn, until about five minutes later, Two large trucks with S.H.I.E.L.D logos on the side pulled up to the gate. The guards kept their guns trained on them. The driver side door on the front one opened, and out stepped a tall, dark skinned man with a shaved head. He walked to the window beside the gate and knocked on the window. The steel wall behind it slid up, revealing a short man with dark hair and glasses.

"Ah agent Pelo," the short man began "Sorry about the less than warm welcome, we heard some sounds of a skirmish in the distance, and I'm afraid that made us a little jumpy."

The dark skinned man replied with a smile "Don't worry, we met up with the other truck on the way here, and one of the rookies panicked, thought it was someone coming here to attack the base or something"

The bespectacled man appeared visibly relieved, but then got a confused expression and said "but we heard something slamming into the truck!"

Agent Pelo seemed puzzled then relaxed and said "Oh that, amid the confusion agent Shilo ran into the truck!"

"I WAS ATTACKED AND SLAMMED INTO THE TRUCK" yelled an angry voice in the truck.

"Sure you were Shilo" Pelo said with a laugh, then turned back to the man behind the window "Ignore him, Shilo is just being paranoid again"

"I CAN TELL YOU'RE TALKING ABOUT ME"

The man behind the window laughed "I know, now can I see you ID? I can't let you through without it."

"Oh, right" Pelo said casually, pulling something out of his pocket. It was a small ID card with his face on it.

The man with glasses nodded and pushed a button, opening the gate. "Go on in, the colonel won't be happy if the supplies are late.'

Pelo smiled and said "Thanks, we wouldn't want to make the colonel angry now would we?" as he got back in the truck and drove through the gate. As soon as he was out of hearing range, he turned on his phone and said "we're in"

* * *

The message was received by a computer technician, working on his computer, when he heard in his headset _"we're in" _

He leaned over to the guy on the computer behind him and said "the Mets won last night"

The guy looked a little panicked "you're sure!?"

The first guy nodded. The second guy took a long, slow breath and typed a command into the computer, and all of the base's power went out.

* * *

(Update:8/19/14) I'm really sorry about my update time. I was just about to publish chapter when the computer with the file on it broke. So the file is okay, I just can't get to it yet. I promise it will be up tomorrow, or the day after at the most. Thank you for patience and I am really sorry.


	2. The attack

(A/N: Sorry about the update time, I promise I will be faster from now on. Thank you for your patience)

Agent Pelo and the rest of his team were walking down a hallway when the lights went out. The hallway plunged into darkness, until some glowing red smoke engulfed. By the time the lights turned back on the smoke had dissipated… and the agents were no longer standing there, in their place were a group of spies. They all were wearing red suits and ski masks, there were a few variations, like one in a concierge suit, one with a fedora and one wearing a fez and sunglasses, etc.

The one standing wearing agent Pelo stood took out a black revolver with a white stock and slid against the wall. He reached the corner of the wall and glanced down another hallway. He turned to the others and said with a French accent and said "it is clear"

Concierge spy nodded and turned to the group "all of those with deadringers come forward"

Five spies came forward. Concierge spy nodded and said "you know the plan, head for the east wing."

They each nodded, pulled out a gold stopwatch and headed off.

Concierge spy continued talking "the rest of you, follow me to the command center" he said while pulling out an intricately designed silver revolver.

* * *

The five 'deadringer' spies approached a hallway being patrolled by some guards. The first spy opened the stopwatch and stepped into the hall. He managed to fire his revolver once before the guards noticed him and gunned him down. His cold, limp body laid there, while the dead spy appeared out of thin air with the other spies. The next spy in line smiled and did the same thing. Reappearing behind the other spies.

While the guards were firing at the infinite supplies from the hallway, one the agents activated the alarm. He pulled out a radio and begin to yell "we are under attack in corridor A24, unknown number of adversaries! Send back up!"

* * *

The remaining spies calmly cloaked as a squad of troops ran by to the conflict.

One of the spies laughed "fools" he said, one of the others shushed him. Concierge spy looked down another hallway.

"There" he whispered, pointing at a glass sliding door. They were again engulfed in red smoke, and in there stead stood the agents. They ran to the door, faking panic. Pelo swiped his ID and opened the door.

Four technicians and two guards were in the control room. What's going on" Pelo yelled. One of the guards answered him. "There was an attack in the west wing, they sent nearly everyone, we were just left behind to guard the command center."

Pelo nodded and looked at two of the technicians, and nodded. All of them drew their revolvers. The four non spies didn't stand a chance.

* * *

One of the technicians, who had now dropped his disguise, was hacking into the main computer. He place a grey rectangle with a blue panel on it, and the entire computer sparked and burst with electricity. When it turned on it showed a map of America, and something on it was labeled B.U.S location.

Concierge spy smiled "we found it boys, time for our best man" he said, looking at a spy in only a suit and mask. The spy smiled and opened a white PDA and pulled out a cigarette. He lit it and smiled, "Lets begin"


	3. Chapter 3

(sorry about lack of updates, it will pick up from here)

A week later

"…so if we reroute the coupling system…" "…we can create a feedback loop…"

"…we can nullify the function leak!" the yelled together.

Agent Coulson turned to Ward and asked "when did you lose track"

Ward smirked "about ten minutes ago"

Simmons looked confused, "but we had just started talking ten minutes ago."

Exactly" said Skye from the door.

Coulson and Ward laughed while Simmons sarcastically went "ha ha, really clever skye"

Skye grinned "it's a gift"

Fitz raised his eyebrows "I don't see you fixed the plane"

"Oh, so that's what you were doing" said Ward

"Yes" Fitz said exasperated "weren't you listening?"

"No, not really" he replied

Simmons sighed, "We found a way to fix the fuel leak"

"We have a fuel leak?" asked Coulson

"Exactly!" Fitz exclaimed "nobody knew about it, we found about it by accident, we had some kind of glitch in the valve system. There was steam everywhere"

Simmons nodded "When we input the new system, we be able to fly non-stop for days, even weeks, without refueling."

Coulson nodded approvingly, "good work guys. Remind me To get you some help implementing that when we get there."

Skye raised her hand, "hate to be the ignorant rookie but, where are we going?"

We are on our way to the HUB to brief on our next mission, and to find out what SHEILD knows about the attack on the research facility last week."

Ward perked up "I heard about that. What do we know?"

"Nothing other than it was attacked by a large number of men in red suits and masks"

"A cult maybe?" Skye asked

"No, too organized" said Fitz. Simmons nodded, "usually cults are unorganized and anarchic" Fitz finished "these guys were far too organized and skilled."

In a small, dark room, the red spy looked at something in his white PDA, he took out a small piece of paper and glanced at it and nodded "I'm ready" he said, just before the janitor opened the door.

There was a thump, and the man fell to the floor, he was pulled in, and red smoke poured out of the closet. Then the janitor stepped out of the closet, closed the door, and walked out of the hall.

The landing ramp lowered as the plane landed in the hanger. Coulson's team walked into the hanger, except Coulson, who looked at the technicians boarding the plane and said "don't touch Lola"

Then he got off the plane

Skye turned to him as he got off the plane "so what will the rest of us doing while you're in your secret meeting?'

He smiled "actually, you guys get to come to this one"

"What?"

"This has deemed a large enough threat that you should see it, and it doesn't contain any sensitive material, so far"

"Really?"

"These guys came out of nowhere, we need to be ready, anyone at risk is to be briefed, and that includes you guys."

Victoria hand glared at Coulson as his team walked into the briefing room.

"I thought I was clear that this was a level eight meeting."

Coulson smiled "and I thought fury was clear that this is a threat large enough that everyone in danger should know, and that includes my team"

Hand just glared as two agents walked in.

The taller one walked over to ward shook his hand, then embraced him.

He laughed as he pulled back

"Good to see you son"

Ward grinned "good to see you sir"

The man turned to Coulson "so how's the zombie doing?

Coulson smiled "pretty good, considering the circumstances" he nodded to the dark skinned man who had come in as well "is that your new trainee?"

The first man tsked "where are my manners, Coulson, ward, random people with Coulson I don't know, this is agent Triplett."

The dark skinned man shook Coulson's hand "nice to meet you sir."

Coulson gestured to the rest of his team "nice to meet you, this is agents may, Fitz and Simmons. Skye and you already know ward. Team, this is agent Garrett, wards former SO."

Hand grimaced "if we're done with all the icebreaking, can we get started?"

Garrett grinned at her "we're still waiting for Sitwell,"

That moment, a bald man with glasses ran into the room "sorry I'm late, there was an incident down in Special Research."

Hand sniffed "excusable enough, now we have limited information on the attack or the assassins who were responsible, but not long after the attack we received an anonymous tip and contact information."

"From who?" Skye asked incredulously

Hand glared at her. "I will not be interrupted by a insolent fugitive"

Skye snorted "and I will not listen to a stuffed bigwig with a….."

"Okay" Coulson interrupted "calm down, both of you, Hand, who does the information lead too?"

With a glare at Skye she said "that's the problem we don't know, the information doesn't match any way of communicating that we know of"

She turned the holoscreen on and pulled something up. It was just a string of numbers and letters.

Fitz and Simmons glanced at each other, then Fitz said "have you tried the tuefort code?"

Everyone looked at them like they had two heads.

Simmons sighed "the tuefort code involves taking the third digit in every set of five and.." looking at their blank stares she sighed again and said "let us do it"

It took them five minutes.

"Done" Fitz declared, as an image fizzled to life on the screen

Everyone jumped back, because the screen showed a man wearing a terrifying black gas mask and a red jumpsuit, pointing a flame thrower at the screen, he lifted the flamethrower over his head, laughing manically.

"Okay that's enough pyro."

"mmph?"

A man wearing overalls, goggles, and a construction helmet came on screen, shooing away the 'pyro' "here, go play with some matches."

"MMMPH!"

He turned to the agents "sorry about that, he gets a kick out of doing that to people."

Who are you people?" Coulson asked

The man in overalls laughed "sorry, I am the engineer for a humble team of mercenaries, known for our grace and etiquette"

Somewhere, something exploded, followed by laughter.

Engineer smiled, "regardless, are you S.H.E.I.L.D?"

The agents just glanced at each other nervously.

Engineer sighed "okay, assuming you are shield, I have grave news for you."

In the background, a young man wearing a red t-shirt and sweatpants walked to the counter, looked around, and picked up a sandwich.

Engineer continued "One of our number, a master of disguise and assassination, has gone AWOL. We believe he is targeting some of you, and…"

He paused listening to the chewing behind him. "oh no."

SCOOOOOOOOUUUUUTTTTT. YOU ARE DEAD" yelled a large Russian man as he ran for scout."

Chaos ensued, fire, explosions, yelling, the camera was knocked to the ground.

A tall man with black hair, glasses and a lab coat picked it up. He spoke with a German accent. "Um… ja, ve'll have to get back to you, scout ate heavy's sandvich."

Then the screen shutoff.

Coulson was the first to speak "okay, on that note, do we have any other info on the attack?"

Hand shook her head, "no, that was our most concrete lead, every other one is a fake or not informative enough."

Coulson rubbed his temples. "Okay, we have no leads and you called us here for one maybe lead?"

Hand replied indignantly "of course not, we have a lot more to go over…"

TWO HOURS LATER

…and Coulson, they have something for you at the triskelion. You need to pick it go there."

Garrett perked for the first time in an hour. "The triskelion? Me and a couple of other guys need a lift there, do you think you could lend a hand?

Sitwell spoke as well "if it's not too much to ask, I'm headed there as well, and have yet to find good transport.

Coulson nodded "happy to have you aboard. Just meet us by our plane after the meeting."

He looked at hand "it is almost over right?"  
she sighed "yes, that was the last thing on the agenda."

"Finally!" Garrett exclaimed as he left.

Coulson walked up to Fitzsimmons, who had left with Skye, and Triplett, who had left over an hour and a half ago.

"is the new fuel system ready'

"Yes'' they said in unison

"good, we have a few extra passengers today,"

"What for?"

"Just the same destination, Garrett and Triplett are among them." He said with a smile

They nodded as garret walked up with Triplett and a few others. "Thanks Coulson, I owe you one."

"it's nothing, come on, we're leaving soon."

He led the men up the boarding ramp. But one passed a large shipping crate. A hand reached out, grabbed and pulled him out of sight. He stepped back out among red smoke, and hurried up the ramp with Sitwell.

(sorry again, action begins next chapter!)


	4. First victims

(Sorry about the update time, It just was hard to write for a while, with school and all that. I promise I will be faster from now on. Thank you for your patience.)

Most of the people on the BUS were gathered in the main area, awaiting instructions, Coulson was a high ranking officer, and no one wanted to make him mad.

Coulson, sensing such thoughts, called everyone's attention.

"welcome everyone, please make yourself comfortable, I know there are some rumors about me being a full of myself stuffed shirt, and I want to dispel those rumors, so ignore everything Hand has ever said about me."

The entire group laughed.

Coulson smiled "please make yourself comfortable, we have food, we have alcohol, movie collections. Just be careful, my lab team will kill me if I scratch their movies."

Their laughter put them at ease. Coulson was different, they realized. They began to disperse and mingle, some went to the kitchens looking for said food and booze.

Garrett walked up to Coulson "you are the best boss any agent could want."

Coulson smiled. "There's no reason I need to be enemies with the lower ranks."

They shared a laughed as a young agent walked up. "Excuse me sir, where are the restrooms?"

Coulson turned and pointed down the hall. "Third on the left.

"Thanks, and what's with all the security cameras?"

Coulson waved it off "just paranoid regulations, there are none in the restrooms.'

The man sighed in relief "thank you"

"No problem" garret laughed, as the young left he whispered to Coulson "rookie"

"Garrett!"

* * *

The agent went into the bathroom, looked around, and sighed. Red smoke engulfed him and suddenly he was gone, and the red spy was standing in his place.

* * *

Looked around, straightened his tie and opened PDA. Smoke engulfed him, and suddenly he was Ward. He flushed and left the room.

Fitz and Simmons were working on something in the lab when ward walked in. They looked up their lab station. "What do you need ward?" they asked together.

He glanced up at a camera on the ceiling. "Where are all the cameras controlled?"

Fitz looked at the camera on the ceiling, "those? The third computer bank behind the cockpit, why?"

Grant shrugged "no reason" as he left

Fitz and Simmons looked at each other "that was weird" Simmons commented

"And probably some kind of foreshadowing" he shrugged and went back to work

* * *

Ward opened the door to the electronics room. He glanced down the hallway, before walking in, he pulled out a device with a blue panel on it, and placed it on a bank of computers. There was a shower of sparks, then silence.

On every camera in the plane, a green light turned red, then green again.

* * *

Simmons lifted her head, looking at Fitz from across the lab. She stared for a minute, lost in thought, before shaking her head and calling him "Fitz, how long until the centrifuge is finished?"

He glanced at her, "about 10 minutes, why?"

"Just seeing if I have enough time to use the loo real quick." She answered as she headed out the door.

* * *

Spy was sneaking down the hallway when he heard a flush from behind a nearby door. He slid against the wall and tapped his watch. His body turned a vague metallic red before disappearing.

The door opened and Simmons walked out, wiping her hands on a paper towel. She turned down the hallway, missing Spy by inches. As she walked away, Spy faded back into sight. He smiled evilly, as red smoke formed round him.

* * *

Simmons was walking past the living quarters when she heard something.

"Simmons!" Fitz whispered from behind her "Simmons!"

She turned, surprised. "Fitz? What are you doing here?"

"We can't talk here" he said as ushered her into his quarters.

He glanced around nervously, "everyone on the plane is in danger,"

What are you talking about?" she asked, hands on her hips "did Skye put you up to this? She's always doing something like that."

"No "he said, his eyes darting around fearfully "I'm serious."

Her eyes widened 'how badly?"

"I don't know, but do you remember the security feed we found from when the research facility was attacked?" When she nodded he continued "you know how they killed many agents by stabbing them in the back?" She nodded fearfully.

Fitz held up a bloody butterfly knife. "I found someone in the broom closet with this embedded in their back"

Simmons began to panic, "have you told Coulson or someone about this?"

He shook his head "we can't trust anyone."

She blinked in confusion "why can't we trust the rest of the team?"

H pulled out a phone "because this" he started a video. It showed a hallway in some shield base. It showed the red spy next to a elevator, smoking, there was a ding from the elevator. He tossed away his cigarette and was engulfed by red smoke, when it cleared, Coulson was standing there.

"He could be anyone on the plane,' Simmons whispered "Coulson, ward, Skye…"

"Me…" Fitz said "What!?" Simmons exclaimed

Fitz laughed, "oh silly little girl" he said as he spun the butterfly knife, stopping with it pointed toward Simmons.

"What are you doing Fitz? "Simmons asked, panicked, as she backed against the wall.

He laughed as he pinned her against the wall, his knife against her throat "Haven't you figured it out yet? I am not your little sweetheart Fitz." red smoke appeared from nowhere and engulfed him, it cleared to reveal the spy.

* * *

Simmons stepped out of the room calmly, she brushed herself off before walking off.

Fitz looked up as Simmons walked into the lab. He smiled at her, then frowned "you okay?"

She waved it off "yeah, just lost in thought, it's nothing."

He nodded, then gestured to the table "five minutes left on the centrifuge,"

She perked up "good, I want to show you something, follow me."

* * *

She led him to her quarters, pausing at the door. She looked down the hallway before turning to Fitz. "You trust me, right?" she asked

"More than anyone" he answered

"Good" she said as she raised the revolver to his head.

He started, stepping backward "Simmons, what is going on?"

She motioned to the door "get in there"

Eyes glistening he walked towards her. She shoved him in. He fell onto someone. "Fitz?" he heard Simmons ask. He looked up into her eyes. There were tears in them. Confused, he looked back at the door. Simmons was gone, replace by Spy. He smiled evilly, as he turned into Coulson. With a laugh that didn't match Coulson at all, he closed the door and locked them in.


End file.
